Markers + reference

Pilosella

5 species · Asteraceae · Asterales

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Species 5
Genome length 153–153 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnC-GCA-petN LSC 838 0.0105 1.00 46.1 yes View details
psbM-trnD-GUC LSC 678 0.0106 1.00 50.7 yes View details
trnR-UCU-trnG-UCC LSC 298 0.0142 0.95 45.4 yes View details
trnF-ndhJ LSC 585 0.0092 1.00 57.7 yes View details
petA-psbJ LSC 837 0.0103 0.99 58.8 yes View details
psbE-petL LSC 1327 0.0046 0.99 59.2 yes View details
petD LSC 1188 0.0030 1.00 33.6 yes View details
ycf1 IRb 495 0.0040 1.00 37.8 no View details
ndhF-rpl32 SSC 1128 0.0068 0.99 52.4 yes View details
rpl32-trnL SSC 850 0.0096 0.98 46.0 yes View details
ccsA SSC 969 0.0017 1.00 31.4 yes View details
ycf1 SSC 5085 0.0062 1.00 35.8 yes View details
ndhD-psaC SSC 97 0.0247 1.00 60.1 yes View details
rpl20-rps12 LSC 766 0.0048 0.98 57.8 yes View details
rps16 LSC 1116 0.0023 1.00 54.8 yes View details
rps12-ycf15 IRb 983 0.0008 0.98 53.7 yes View details
ycf15-rps12 IRa 983 0.0008 0.98 53.7 yes View details
atpI-atpH LSC 1143 0.0021 1.00 53.2 yes View details
ycf3-trnS LSC 912 0.0066 0.97 53.1 yes View details
psaA-ycf3 LSC 740 0.0052 0.99 52.3 yes View details
petN-psbM LSC 476 0.0092 1.00 50.2 yes View details
trnG-trnfM LSC 196 0.0163 1.00 49.7 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 AGAAATCACTATCCTACCCTTAGT TCTCTGTACCGACTGAACCA 1237 1.000 40.4
rps16_p2 rps16 AGAAATCACTATCCTACCCT TCTCTGTACCGACTGAACCA 1237 1.000 40.4
rps16_p3 rps16 AGAAATCACTATCCTACCCTT TCTCTGTACCGACTGAACCA 1237 1.000 40.4
rps16_p4 rps16 AGAAATCACTATCCTACCCTTAGTT TCTCTGTACCGACTGAACCA 1237 1.000 40.4
rps16_p5 rps16 AGAAATCACTATCCTACCCTTAGT GTCTCTGTACCGACTGAACC 1238 1.000 40.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 894–957 1.000 81.1
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 912–975 1.000 78.8
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 893–956 1.000 75.1
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 902–965 1.000 75.0
trnC-GCA-petN_p5 trnC-GCA-petN TCAGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 951–1014 0.800 66.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 637–658 1.000 61.0
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 637–658 1.000 59.3
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 638–659 1.000 55.1
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 629–650 1.000 55.0
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 623–644 1.000 54.3
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 782–796 1.000 53.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 776–790 1.000 53.2
psbM-trnD-GUC_p3 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TCCCCTGGGATTGTAGTTCA 798–812 1.000 52.8
psbM-trnD-GUC_p4 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TCCCCTGGGATTGTAGTTCA 792–806 1.000 52.4
psbM-trnD-GUC_p5 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 779–793 1.000 52.2
atpI-atpH_p1 atpI-atpH TCCCTGTCATGTTCCTTGGA ATAACGGAAGCGGCAGAAAT 1275–1279 1.000 78.2
atpI-atpH_p2 atpI-atpH TCCCTGTCATGTTCCTTGGA AGCCAATCCAGCAGCAATAA 1291–1295 1.000 77.4
atpI-atpH_p3 atpI-atpH TCCCTGTCATGTTCCTTGGA AATAACGGAAGCGGCAGAAA 1276–1280 1.000 77.1
atpI-atpH_p4 atpI-atpH TCCCTGTCATGTTCCTTGGA GCCAATCCAGCAGCAATAAC 1290–1294 1.000 76.8
atpI-atpH_p5 atpI-atpH TCCCTGTCATGTTCCTTGGA TCCAGCAGCAATAACGGAAG 1285–1289 1.000 76.5
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 366–378 1.000 69.5
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 369–381 1.000 69.3
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 372–384 1.000 68.8
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 375–387 1.000 68.6
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 370–382 1.000 67.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Pilosella cymosa OR909644.1 153258 View on NCBI ↗
Pilosella hoppeana OR909645.1 152924 View on NCBI ↗
Pilosella lactucella OR909646.1 152830 View on NCBI ↗
Pilosella officinarum OR909647.1 153177 View on NCBI ↗
Pilosella sphaerocephala OR909648.1 152866 View on NCBI ↗